Infectious Diseases in Context

Scatter Quadrant

Photo by Aaron Blanco Tejedor on Unsplash

Be safe, be smart, be kind…
— Dr. Tedros Adhanom Ghebreyesus, WHO Director General

Infectious diseases are diseases that are caused by germs. As we’ll see with the data, these germs can be passed on in several different ways from direct and indirect contact, insect or animal bites, or through contaminated food, water, soil, or plants. The data will also indicate the type of pathogen such as bacteria, virus, or parasite. For this case we’ll explore the many different germs and two key areas of interest: how contagious they are and the fatality rate if infected.

Ingest data

Disease, R0, Fatality Rate, and Mode of Transmission

df = read.csv("archetypes/infectious-disease/infectious-disease.csv", header = TRUE, stringsAsFactors = FALSE)
df

Wrangle data

Rename, select, clean, and cast data types

# Simplify the column names
df_complete <- rename(df, 
                      DISEASE = "Disease_Name", 
                      PATHOGEN = "Pathogen.type",
                      CONTAGIOUSNESS = "R0", 
                      DEADLINESS = "Case_Fatality_Rate_Percent", 
                      TRANSMISSION = "Primary_Mode_of_Transmission")

# Select only the needed
df_complete <- select(df_complete, c("N", "DISEASE", "PATHOGEN", "CONTAGIOUSNESS", "DEADLINESS", "TRANSMISSION"))

# Make sure all visual variables are proper data types
df_complete$CONTAGIOUSNESS <- as.numeric(df_complete$CONTAGIOUSNESS)
df_complete$DEADLINESS <- parse_number(df_complete$DEADLINESS)

# Make sure we don't factor empty strings
df_complete <- filter(df_complete, nchar(PATHOGEN) > 0)
df_complete <- filter(df_complete, nchar(TRANSMISSION) > 0)
# Factor the string fields
df_complete$PATHOGEN <- as.factor(df_complete$PATHOGEN)
df_complete$TRANSMISSION <- as.factor(df_complete$TRANSMISSION)

# Remove incomplete cases
df_complete <- df_complete[complete.cases(df_complete), ]
df_complete <- filter(df_complete, is.na(DEADLINESS) == FALSE)

df_complete

Base Scatter Plot

Position, Shape, Color

# theme parameters
theme_opts <- theme(
  text = element_text(family = "inconsolata"), 
  legend.position = "none",
  legend.title = element_blank(),
  #axis.text = element_blank(),
  #axis.line = element_blank(),
  #axis.ticks = element_blank(),
  #axis.title = element_blank(),
  #panel.grid = element_blank(),
  panel.grid.major = element_line(linetype = "dotted"),
  panel.grid.minor = element_blank(),
  panel.background = element_rect(fill="white", colour="white"),
  #panel.border = element_blank(),
  plot.background = element_rect(fill="white", colour="white"),
  plot.margin = unit(c(0.5,2,1,0.5), "in")
)

# Print values needed for mapping
# as.data.frame(unique(df_complete$PATHOGEN))
shape_mapping <- c("bacterium" = 23, "virus" = 21, "parasite" = 24, "prion" = 22)

# Print values needed for palette
# as.data.frame(unique(df_complete$TRANSMISSION))
transmission_palette <- c("airborne" = "#c62828", 
                          "bite" = "#ad1457", 
                          "fecal-oral" = "#6a1b9a", 
                          "food" = "#4527a0", 
                          "body fluids" = "#4527a0",
                          "parasite" = "#1565c0",
                          "waterborne" = "#0277bd",
                          "airborne, fecal-oral" = "#00838f",
                          "sexual contact" = "#00695c",
                          "airborne, body fluids" = "#558b2f",
                          "fecal-oral, surfaces" = "#f9a825",
                          "bite, sexual contact" = "#ef6c00")

v1 <- ggplot(df_complete) +
      annotate("rect", xmin = 0, xmax = 17, ymin = 0, ymax = 1, fill = "#f0f0f0", alpha = 0.2) +
      annotate("rect", xmin = 0, xmax = 17, ymin = 20, ymax = 50, fill = "#f0f0f0", alpha = 0.2) +
      geom_point_interactive(aes(x = CONTAGIOUSNESS, 
                 y = DEADLINESS, 
                 shape = PATHOGEN,
                 fill = TRANSMISSION,
                 tooltip = paste0("Disease: ", DISEASE, "\n", "Deadliness: ", DEADLINESS, "%\n", "Contagiousness: ", CONTAGIOUSNESS, "\n", "Transmission: ", TRANSMISSION),
                 data_id = N), 
                 color='#ffffff', size = 3.0, alpha = 1.0 ) +
      geom_text_repel(aes(x = CONTAGIOUSNESS, 
                 y = DEADLINESS, 
                 label = DISEASE, color = TRANSMISSION), family = 'inconsolata', size = 4, force = 0.5, nudge_x = 0.25, segment.size  = 0.2, segment.color = "grey50", direction = "y", hjust = 0) +
      #expand_limits(x = 0.1, y = 0.1) +
      scale_x_continuous(limits = c(0,17), breaks = seq(0, 17, 1), labels = seq(0, 17, 1)) +
      scale_y_continuous(trans = "log2", 
                         breaks = c(0, 0.1, 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100), 
                         labels = c(0, 0.1, 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100),
                         expand = c(0, 0)) +
      scale_shape_manual(values = shape_mapping) +
      scale_fill_manual(values = transmission_palette) +
      scale_color_manual(values = transmission_palette) +
      coord_cartesian(clip = 'off') +
      labs(x="CONTAGIOUSNESS",
         y="DEADLINESS",
         title = NULL) +
      theme_minimal(base_family = "inconsolata", base_size = 16) +
      theme_opts

girafe(ggobj = v1, width_svg = 1280/72, height_svg = 720/72,
       options = list(
         opts_sizing(rescale = TRUE, width = 1.0), 
         opts_hover_inv(css = "opacity:0.2;"), 
         opts_hover(css = "fill:black;")
         )
      )

The Quadrant

and annotations…

v2 <- v1 + geom_vline(xintercept = 1) +
  geom_vline(xintercept = 5) +
  geom_vline(xintercept = 7) +
  geom_vline(xintercept = 12) +
  geom_vline(xintercept = 17) +
  # X axis quadrants
  annotate("text", x = 0, y = 100, 
           label = "not very", 
           hjust = 0.5, vjust=-2.0, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 3, y = 100, 
           label = "quite contagious", 
           hjust = 0.5, vjust=-2.0, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 6, y = 100, 
           label = "very", 
           hjust = 0.5, vjust=-2.0, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 9.5, y = 100, 
           label = "extremely", 
           hjust = 0.5, vjust=-2.0, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 14.5, y = 100, 
           label = "hide", 
           hjust = 0.5, vjust=-2.0, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  # Y axis quadrants
  annotate("text", x = 17, y = 80, 
           label = "  extremely deadly", 
           hjust=0, vjust=0.5, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 80, 
           label = "   death likely", 
           hjust=0, vjust=2.5, size = 4, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 35, 
           label = "  deadly", 
           hjust=0, vjust=0.5, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 35, 
           label = "   high chance of death", 
           hjust=0, vjust=2.5, size = 4, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 5, 
           label = "  quite deadly", 
           hjust=0, vjust=0.5, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 5, 
           label = "   unlucky or unhealthy", 
           hjust=0, vjust=2.5, size = 4, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 0.35, 
           label = "  not too deadly", 
           hjust=0, vjust=0.5, size = 5, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  annotate("text", x = 17, y = 0.35, 
           label = "   high risk groups\n   (i.e. infants, elderly)", 
           hjust=0, vjust=1.5, size = 4, color = "#bbbbbb", family = "inconsolata", fontface = 1) +
  # Axis annotation
  annotate("text", x = 1, y = 0, 
           label = "Ro = 1\nDisease not\nlikely to spread)",
           hjust=0, vjust=1.5, size = 4, color = "#bbbbbb", family = "inconsolata", fontface = 1)
  # Quadrant rectangles
  # But this will place as a top layer
  # So we move it to the bottom of the layer build up
  # annotate("rect", xmin = 0, xmax = 17, ymin = 0, ymax = 1, fill = "#f0f0f0", alpha = 0.2) +
  # annotate("rect", xmin = 0, xmax = 17, ymin = 20, ymax = 50, fill = "#f0f0f0", alpha = 0.2)


girafe(ggobj = v2, width_svg = 1280/72, height_svg = 720/72,
       options = list(opts_sizing(rescale = TRUE, width = 1.0))
      )

References

citations for narrative and data sources

Narrative inspiration and data sources: The MicrobeScope Infectious Diseases in Context, GO